[2023-06-05 15:04:30,736] [INFO] DFAST_QC pipeline started.
[2023-06-05 15:04:30,739] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 15:04:30,740] [INFO] DQC Reference Directory: /var/lib/cwl/stg07775729-f60c-4a40-ad06-46b54daee933/dqc_reference
[2023-06-05 15:04:31,945] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 15:04:31,946] [INFO] Task started: Prodigal
[2023-06-05 15:04:31,946] [INFO] Running command: gunzip -c /var/lib/cwl/stg002cf5e6-e9c1-4b44-8d3b-8ef1a704f2bc/GCA_004294385.1_ASM429438v1_genomic.fna.gz | prodigal -d GCA_004294385.1_ASM429438v1_genomic.fna/cds.fna -a GCA_004294385.1_ASM429438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 15:04:44,896] [INFO] Task succeeded: Prodigal
[2023-06-05 15:04:44,896] [INFO] Task started: HMMsearch
[2023-06-05 15:04:44,897] [INFO] Running command: hmmsearch --tblout GCA_004294385.1_ASM429438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07775729-f60c-4a40-ad06-46b54daee933/dqc_reference/reference_markers.hmm GCA_004294385.1_ASM429438v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 15:04:45,273] [INFO] Task succeeded: HMMsearch
[2023-06-05 15:04:45,275] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg002cf5e6-e9c1-4b44-8d3b-8ef1a704f2bc/GCA_004294385.1_ASM429438v1_genomic.fna.gz]
[2023-06-05 15:04:45,333] [INFO] Query marker FASTA was written to GCA_004294385.1_ASM429438v1_genomic.fna/markers.fasta
[2023-06-05 15:04:45,334] [INFO] Task started: Blastn
[2023-06-05 15:04:45,334] [INFO] Running command: blastn -query GCA_004294385.1_ASM429438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07775729-f60c-4a40-ad06-46b54daee933/dqc_reference/reference_markers.fasta -out GCA_004294385.1_ASM429438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 15:04:46,001] [INFO] Task succeeded: Blastn
[2023-06-05 15:04:46,007] [INFO] Selected 16 target genomes.
[2023-06-05 15:04:46,007] [INFO] Target genome list was writen to GCA_004294385.1_ASM429438v1_genomic.fna/target_genomes.txt
[2023-06-05 15:04:46,011] [INFO] Task started: fastANI
[2023-06-05 15:04:46,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg002cf5e6-e9c1-4b44-8d3b-8ef1a704f2bc/GCA_004294385.1_ASM429438v1_genomic.fna.gz --refList GCA_004294385.1_ASM429438v1_genomic.fna/target_genomes.txt --output GCA_004294385.1_ASM429438v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 15:05:01,406] [INFO] Task succeeded: fastANI
[2023-06-05 15:05:01,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07775729-f60c-4a40-ad06-46b54daee933/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 15:05:01,407] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07775729-f60c-4a40-ad06-46b54daee933/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 15:05:01,417] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 15:05:01,417] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 15:05:01,418] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Argonema galeatum	strain=A003/A1	GCA_023333595.1	2942762	2942762	type	True	76.3141	193	1876	95	below_threshold
Planktothrix agardhii	strain=NIES-204	GCA_003609755.1	1160	1160	type	True	76.2458	97	1876	95	below_threshold
Argonema antarcticum	strain=A004/B2	GCA_023333585.1	2942763	2942763	type	True	76.2244	194	1876	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	75.7083	82	1876	95	below_threshold
Oscillatoria acuminata	strain=PCC 6304	GCA_000317105.1	118323	118323	type	True	75.6973	105	1876	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	75.6783	80	1876	95	below_threshold
Gloeocapsopsis dulcis	strain=AAB1	GCA_002964865.1	2859516	2859516	type	True	75.5896	60	1876	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	75.3737	101	1876	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 15:05:01,420] [INFO] DFAST Taxonomy check result was written to GCA_004294385.1_ASM429438v1_genomic.fna/tc_result.tsv
[2023-06-05 15:05:01,421] [INFO] ===== Taxonomy check completed =====
[2023-06-05 15:05:01,421] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 15:05:01,421] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07775729-f60c-4a40-ad06-46b54daee933/dqc_reference/checkm_data
[2023-06-05 15:05:01,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 15:05:01,489] [INFO] Task started: CheckM
[2023-06-05 15:05:01,490] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004294385.1_ASM429438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004294385.1_ASM429438v1_genomic.fna/checkm_input GCA_004294385.1_ASM429438v1_genomic.fna/checkm_result
[2023-06-05 15:05:44,498] [INFO] Task succeeded: CheckM
[2023-06-05 15:05:44,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 15:05:44,536] [INFO] ===== Completeness check finished =====
[2023-06-05 15:05:44,537] [INFO] ===== Start GTDB Search =====
[2023-06-05 15:05:44,538] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004294385.1_ASM429438v1_genomic.fna/markers.fasta)
[2023-06-05 15:05:44,538] [INFO] Task started: Blastn
[2023-06-05 15:05:44,538] [INFO] Running command: blastn -query GCA_004294385.1_ASM429438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07775729-f60c-4a40-ad06-46b54daee933/dqc_reference/reference_markers_gtdb.fasta -out GCA_004294385.1_ASM429438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 15:05:45,369] [INFO] Task succeeded: Blastn
[2023-06-05 15:05:45,373] [INFO] Selected 12 target genomes.
[2023-06-05 15:05:45,374] [INFO] Target genome list was writen to GCA_004294385.1_ASM429438v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 15:05:45,382] [INFO] Task started: fastANI
[2023-06-05 15:05:45,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg002cf5e6-e9c1-4b44-8d3b-8ef1a704f2bc/GCA_004294385.1_ASM429438v1_genomic.fna.gz --refList GCA_004294385.1_ASM429438v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004294385.1_ASM429438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 15:06:18,656] [INFO] Task succeeded: fastANI
[2023-06-05 15:06:18,667] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 15:06:18,667] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_004294385.1	s__Microcoleus sp004294385	100.0	1861	1876	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	99.93	99.93	0.96	0.96	2	conclusive
GCF_002412335.2	s__Microcoleus bourrellyi	91.4639	1254	1876	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004292745.1	s__Microcoleus sp004292745	87.4729	1341	1876	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	99.54	99.38	0.91	0.88	6	-
GCA_003542015.1	s__Microcoleus sp003542015	86.7573	1137	1876	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003003725.1	s__Microcoleus sp003003725	84.795	1245	1876	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	98.42	98.42	0.87	0.87	2	-
GCA_004292955.1	s__Microcoleus sp004292955	83.5433	1358	1876	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	98.97	98.79	0.93	0.91	14	-
GCF_013179805.1	s__Microcoleus asticus	83.4355	1309	1876	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014695295.1	s__Microcoleus sp014695295	83.3634	1305	1876	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012035135.1	s__Microcoleus sp012035135	83.331	1078	1876	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	99.44	99.44	0.86	0.86	2	-
GCF_014695175.1	s__Microcoleus sp014695175	83.1976	1233	1876	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	96.46	96.46	0.87	0.87	3	-
GCF_015207285.1	s__Microcoleus sp015207285	82.9275	1231	1876	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207505.1	s__Microcoleus sp015207505	82.7927	1282	1876	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	96.23	96.23	0.84	0.84	3	-
--------------------------------------------------------------------------------
[2023-06-05 15:06:18,669] [INFO] GTDB search result was written to GCA_004294385.1_ASM429438v1_genomic.fna/result_gtdb.tsv
[2023-06-05 15:06:18,670] [INFO] ===== GTDB Search completed =====
[2023-06-05 15:06:18,674] [INFO] DFAST_QC result json was written to GCA_004294385.1_ASM429438v1_genomic.fna/dqc_result.json
[2023-06-05 15:06:18,675] [INFO] DFAST_QC completed!
[2023-06-05 15:06:18,675] [INFO] Total running time: 0h1m48s